コード例 #1
0
MGSolver_Status _GetSolveStatus( MGSolver_PETScData* mgData ) {
	PC			pc;
	const KSPType		kspType;
	const PCType		pcType;
	KSPConvergedReason	reason;
	PetscErrorCode		ec;

	ec = KSPGetType( mgData->ksp, &kspType );
	CheckPETScError( ec );
	ec = KSPGetPC( mgData->ksp, &pc );
	CheckPETScError( ec );
	ec = PCGetType( pc, &pcType );
	CheckPETScError( ec );

	if( !strcmp( kspType, KSPRICHARDSON ) && !strcmp( pcType, PCSOR ) ) {
		double		rnorm;
		PetscInt	curIt;

		//rnorm = PETScMatrixSolver_GetResidualNorm( self );
		//curIt = PETScMatrixSolver_GetIterations( self );
		rnorm = _GetResidualNorm( mgData );
		KSPGetIterationNumber( mgData->ksp, &curIt );
		//PETScMatrixSolver_SetNormType( self, MultigridSolver_NormType_Preconditioned );
		KSPSetNormType( mgData->ksp, MultigridSolver_NormType_Preconditioned );
		ec = KSPDefaultConverged( mgData->ksp, curIt, (PetscScalar)rnorm, &reason, PETSC_NULL );
		CheckPETScError( ec );
	}
	else {
		ec = KSPGetConvergedReason( mgData->ksp, &reason );
		CheckPETScError( ec );
	}

	return reason;
}
コード例 #2
0
double _GetResidualNorm( MGSolver_PETScData* mgData ) {
	PC			pc;
	const KSPType		kspType;
	const PCType		pcType;
	PetscScalar		rnorm;
	PetscErrorCode		ec;

	ec = KSPGetType( mgData->ksp, &kspType );
	CheckPETScError( ec );
	ec = KSPGetPC( mgData->ksp, &pc );
	CheckPETScError( ec );
	ec = PCGetType( pc, &pcType );
	CheckPETScError( ec );

	if( !strcmp( kspType, KSPRICHARDSON ) && !strcmp( pcType, PCSOR ) ) {
		Vec	residual;

		//residual = MatrixSolver_GetResidual( mgData );
		//rnorm = (PetscScalar)Vector_L2Norm( residual );
		residual = _GetResidual( mgData );
		VecNorm( residual, NORM_2, &rnorm );
	}
	else {
		ec = KSPGetResidualNorm( mgData->ksp, &rnorm );
		CheckPETScError( ec );
	}

	return (double)rnorm;
}
コード例 #3
0
ファイル: shell.c プロジェクト: OpenCMISS-Dependencies/slepc
PetscErrorCode STSetFromOptions_Shell(ST st)
{
  PetscErrorCode ierr;
  PC             pc;
  PCType         pctype;
  KSPType        ksptype;

  PetscFunctionBegin;
  if (!st->ksp) { ierr = STGetKSP(st,&st->ksp);CHKERRQ(ierr); }
  ierr = KSPGetPC(st->ksp,&pc);CHKERRQ(ierr);
  ierr = KSPGetType(st->ksp,&ksptype);CHKERRQ(ierr);
  ierr = PCGetType(pc,&pctype);CHKERRQ(ierr);
  if (!pctype && !ksptype) {
    if (st->shift_matrix == ST_MATMODE_SHELL) {
      /* in shell mode use GMRES with Jacobi as the default */
      ierr = KSPSetType(st->ksp,KSPGMRES);CHKERRQ(ierr);
      ierr = PCSetType(pc,PCJACOBI);CHKERRQ(ierr);
    } else {
      /* use direct solver as default */
      ierr = KSPSetType(st->ksp,KSPPREONLY);CHKERRQ(ierr);
      ierr = PCSetType(pc,PCREDUNDANT);CHKERRQ(ierr);
    }
  }
  PetscFunctionReturn(0);
}
コード例 #4
0
static PetscErrorCode PCBDDCScalingSetUp_Deluxe_Private(PC pc)
{
  PC_BDDC                *pcbddc=(PC_BDDC*)pc->data;
  PCBDDCDeluxeScaling    deluxe_ctx=pcbddc->deluxe_ctx;
  PCBDDCSubSchurs        sub_schurs = pcbddc->sub_schurs;
  PetscErrorCode         ierr;

  PetscFunctionBegin;
  if (!sub_schurs->n_subs) {
    PetscFunctionReturn(0);
  }

  /* Create work vectors for sequential part of deluxe */
  ierr = MatCreateVecs(sub_schurs->S_Ej_all,&deluxe_ctx->seq_work1,&deluxe_ctx->seq_work2);CHKERRQ(ierr);

  /* Compute deluxe sequential scatter */
  if (sub_schurs->reuse_mumps && !sub_schurs->is_dir) {
    PCBDDCReuseMumps reuse_mumps = sub_schurs->reuse_mumps;
    ierr = PetscObjectReference((PetscObject)reuse_mumps->correction_scatter_B);CHKERRQ(ierr);
    deluxe_ctx->seq_scctx = reuse_mumps->correction_scatter_B;
  } else {
    ierr = VecScatterCreate(pcbddc->work_scaling,sub_schurs->is_Ej_all,deluxe_ctx->seq_work1,NULL,&deluxe_ctx->seq_scctx);CHKERRQ(ierr);
  }

  /* Create Mat object for deluxe scaling */
  ierr = PetscObjectReference((PetscObject)sub_schurs->S_Ej_all);CHKERRQ(ierr);
  deluxe_ctx->seq_mat = sub_schurs->S_Ej_all;
  if (sub_schurs->sum_S_Ej_all) { /* if this matrix is present, then we need to create the KSP object to invert it */
    PC               pc_temp;
    MatSolverPackage solver=NULL;
    char             ksp_prefix[256];
    size_t           len;

    ierr = KSPCreate(PETSC_COMM_SELF,&deluxe_ctx->seq_ksp);CHKERRQ(ierr);
    ierr = KSPSetOperators(deluxe_ctx->seq_ksp,sub_schurs->sum_S_Ej_all,sub_schurs->sum_S_Ej_all);CHKERRQ(ierr);
    ierr = KSPSetType(deluxe_ctx->seq_ksp,KSPPREONLY);CHKERRQ(ierr);
    ierr = KSPGetPC(deluxe_ctx->seq_ksp,&pc_temp);CHKERRQ(ierr);
    ierr = PCSetType(pc_temp,PCLU);CHKERRQ(ierr);
    ierr = KSPGetPC(pcbddc->ksp_D,&pc_temp);CHKERRQ(ierr);
    ierr = PCFactorGetMatSolverPackage(pc_temp,(const MatSolverPackage*)&solver);CHKERRQ(ierr);
    if (solver) {
      PC     new_pc;
      PCType type;

      ierr = PCGetType(pc_temp,&type);CHKERRQ(ierr);
      ierr = KSPGetPC(deluxe_ctx->seq_ksp,&new_pc);CHKERRQ(ierr);
      ierr = PCSetType(new_pc,type);CHKERRQ(ierr);
      ierr = PCFactorSetMatSolverPackage(new_pc,solver);CHKERRQ(ierr);
    }
    ierr = PetscStrlen(((PetscObject)(pcbddc->ksp_D))->prefix,&len);CHKERRQ(ierr);
    len -= 10; /* remove "dirichlet_" */
    ierr = PetscStrncpy(ksp_prefix,((PetscObject)(pcbddc->ksp_D))->prefix,len+1);CHKERRQ(ierr);
    ierr = PetscStrcat(ksp_prefix,"deluxe_");CHKERRQ(ierr);
    ierr = KSPSetOptionsPrefix(deluxe_ctx->seq_ksp,ksp_prefix);CHKERRQ(ierr);
    ierr = KSPSetFromOptions(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
    ierr = KSPSetUp(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
コード例 #5
0
PetscErrorCode BSSCR_pc_warn( PC pc, const char func_name[] ) 
{
	const PCType type;
	PCGetType( pc, &type );
	
	if( strcmp(type,PCTYPE_GtKG)!=0 ) {
		printf("Warning(%s): PC type (%s) should be gtkg \n",func_name, type );
		PetscFunctionReturn(0);
	}
	PetscFunctionReturn(0);
}
コード例 #6
0
PetscErrorCode BSSCR_BSSCR_pc_error_ScGtKG( PC pc, const char func_name[] ) 
{
	const PCType type;
	PCGetType( pc, &type );
	
	if( strcmp(type,PCTYPE_SCGtKG)!=0 ) {
		printf("Error(%s): PC type (%s) should be scgtkg. \n",func_name, type );
		PetscFinalize();
		exit(0);
	}
	PetscFunctionReturn(0);
}
コード例 #7
0
ファイル: mgfunc.c プロジェクト: pombredanne/petsc
/*@
   PCMGGetSmootherUp - Gets the KSP context to be used as smoother after
   coarse grid correction (post-smoother).

   Not Collective, KSP returned is parallel if PC is

   Input Parameters:
+  pc - the multigrid context
-  l  - the level (0 is coarsest) to supply

   Ouput Parameters:
.  ksp - the smoother

   Level: advanced

   Notes: calling this will result in a different pre and post smoother so you may need to
         set options on the pre smoother also

.keywords: MG, multigrid, get, smoother, up, post-smoother, level

.seealso: PCMGGetSmootherUp(), PCMGGetSmootherDown()
@*/
PetscErrorCode  PCMGGetSmootherUp(PC pc,PetscInt l,KSP *ksp)
{
  PC_MG          *mg        = (PC_MG*)pc->data;
  PC_MG_Levels   **mglevels = mg->levels;
  PetscErrorCode ierr;
  const char     *prefix;
  MPI_Comm       comm;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(pc,PC_CLASSID,1);
  /*
     This is called only if user wants a different pre-smoother from post.
     Thus we check if a different one has already been allocated,
     if not we allocate it.
  */
  if (!l) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_ARG_OUTOFRANGE,"There is no such thing as a up smoother on the coarse grid");
  if (mglevels[l]->smoothu == mglevels[l]->smoothd) {
    KSPType     ksptype;
    PCType      pctype;
    PC          ipc;
    PetscReal   rtol,abstol,dtol;
    PetscInt    maxits;
    KSPNormType normtype;
    ierr = PetscObjectGetComm((PetscObject)mglevels[l]->smoothd,&comm);CHKERRQ(ierr);
    ierr = KSPGetOptionsPrefix(mglevels[l]->smoothd,&prefix);CHKERRQ(ierr);
    ierr = KSPGetTolerances(mglevels[l]->smoothd,&rtol,&abstol,&dtol,&maxits);CHKERRQ(ierr);
    ierr = KSPGetType(mglevels[l]->smoothd,&ksptype);CHKERRQ(ierr);
    ierr = KSPGetNormType(mglevels[l]->smoothd,&normtype);CHKERRQ(ierr);
    ierr = KSPGetPC(mglevels[l]->smoothd,&ipc);CHKERRQ(ierr);
    ierr = PCGetType(ipc,&pctype);CHKERRQ(ierr);

    ierr = KSPCreate(comm,&mglevels[l]->smoothu);CHKERRQ(ierr);
    ierr = KSPSetErrorIfNotConverged(mglevels[l]->smoothu,pc->erroriffailure);CHKERRQ(ierr);
    ierr = PetscObjectIncrementTabLevel((PetscObject)mglevels[l]->smoothu,(PetscObject)pc,mglevels[0]->levels-l);CHKERRQ(ierr);
    ierr = KSPSetOptionsPrefix(mglevels[l]->smoothu,prefix);CHKERRQ(ierr);
    ierr = KSPSetTolerances(mglevels[l]->smoothu,rtol,abstol,dtol,maxits);CHKERRQ(ierr);
    ierr = KSPSetType(mglevels[l]->smoothu,ksptype);CHKERRQ(ierr);
    ierr = KSPSetNormType(mglevels[l]->smoothu,normtype);CHKERRQ(ierr);
    ierr = KSPSetConvergenceTest(mglevels[l]->smoothu,KSPConvergedSkip,NULL,NULL);CHKERRQ(ierr);
    ierr = KSPGetPC(mglevels[l]->smoothu,&ipc);CHKERRQ(ierr);
    ierr = PCSetType(ipc,pctype);CHKERRQ(ierr);
    ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)mglevels[l]->smoothu);CHKERRQ(ierr);
    ierr = PetscObjectComposedDataSetInt((PetscObject) mglevels[l]->smoothu, PetscMGLevelId, mglevels[l]->level);CHKERRQ(ierr);
  }
  if (ksp) *ksp = mglevels[l]->smoothu;
  PetscFunctionReturn(0);
}
コード例 #8
0
void SolverLinearPetsc<T>::init ()
{
    // Initialize the data structures if not done so already.
    if ( !this->initialized() )
    {
        this->setInitialized(  true );

        int ierr=0;

        // 2.1.x & earlier style
#if (PETSC_VERSION_MAJOR == 2) && (PETSC_VERSION_MINOR <= 1)

        // Create the linear solver context
        ierr = SLESCreate ( this->worldComm().globalComm(), &M_sles );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        // Create the Krylov subspace & preconditioner contexts
        ierr = SLESGetKSP       ( M_sles, &M_ksp );
        CHKERRABORT( this->worldComm().globalComm(),ierr );
        ierr = SLESGetPC        ( M_sles, &M_pc );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        // Have the Krylov subspace method use our good initial guess rather than 0
        ierr = KSPSetInitialGuessNonzero ( M_ksp, PETSC_TRUE );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        // Set user-specified  solver and preconditioner types
        this->setPetscSolverType();
        this->setPetscPreconditionerType();
        this->setPetscConstantNullSpace();

        // Set the options from user-input
        // Set runtime options, e.g.,
        //      -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
        //  These options will override those specified above as long as
        //  SLESSetFromOptions() is called _after_ any other customization
        //  routines.

        ierr = SLESSetFromOptions ( M_sles );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        // 2.2.0 & newer style
#else

        // Create the linear solver context
        ierr = KSPCreate ( this->worldComm().globalComm(), &M_ksp );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        // Create the preconditioner context
        ierr = KSPGetPC        ( M_ksp, &M_pc );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        // Have the Krylov subspace method use our good initial guess rather than 0
        ierr = KSPSetInitialGuessNonzero ( M_ksp, PETSC_TRUE );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        // Set user-specified  solver and preconditioner types
        this->setPetscSolverType();
        this->setPetscConstantNullSpace();


        // Set the options from user-input
        // Set runtime options, e.g.,
        //      -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
        //  These options will override those specified above as long as
        //  KSPSetFromOptions() is called _after_ any other customization
        //  routines.
        //ierr = PCSetFromOptions ( M_pc );
        //CHKERRABORT( this->worldComm().globalComm(),ierr );
        ierr = KSPSetFromOptions ( M_ksp );
        CHKERRABORT( this->worldComm().globalComm(),ierr );


#endif

        // Have the Krylov subspace method use our good initial guess
        // rather than 0, unless the user requested a KSPType of
        // preonly, which complains if asked to use initial guesses.
#if PETSC_VERSION_LESS_THAN(3,0,0)
        KSPType ksp_type;
#else
#if PETSC_VERSION_LESS_THAN(3,4,0)
        const KSPType ksp_type;
#else
        KSPType ksp_type;
#endif
#endif

        ierr = KSPGetType ( M_ksp, &ksp_type );
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        if ( std::string((char*)ksp_type) == std::string( ( char* )KSPPREONLY ) )
        {
            ierr = KSPSetInitialGuessNonzero ( M_ksp, PETSC_FALSE );
            CHKERRABORT( this->worldComm().globalComm(),ierr );
        }

        if ( std::string((char*)ksp_type) == std::string( ( char* )KSPGMRES ) )
        {
            int nRestartGMRES = option(_name="gmres-restart", _prefix=this->prefix() ).template as<int>();
            ierr = KSPGMRESSetRestart( M_ksp, nRestartGMRES );
            CHKERRABORT( this->worldComm().globalComm(),ierr );
        }
        // Notify PETSc of location to store residual history.
        // This needs to be called before any solves, since
        // it sets the residual history length to zero.  The default
        // behavior is for PETSc to allocate (internally) an array
        // of size 1000 to hold the residual norm history.
        ierr = KSPSetResidualHistory( M_ksp,
                                      PETSC_NULL,   // pointer to the array which holds the history
                                      PETSC_DECIDE, // size of the array holding the history
                                      PETSC_TRUE ); // Whether or not to reset the history for each solve.
        CHKERRABORT( this->worldComm().globalComm(),ierr );

        //If there is a preconditioner object we need to set the internal setup and apply routines
        if ( this->M_preconditioner )
        {
            VLOG(2) << "preconditioner: "  << this->M_preconditioner << "\n";

            PCSetType(M_pc, PCSHELL);
            PCShellSetName( M_pc, this->M_preconditioner->name().c_str() );
            PCShellSetContext( M_pc,( void* )this->M_preconditioner.get() );
            PCShellSetSetUp( M_pc,__feel_petsc_preconditioner_setup );
            PCShellSetApply( M_pc,__feel_petsc_preconditioner_apply );
            PCShellSetView( M_pc,__feel_petsc_preconditioner_view );
#if PETSC_VERSION_LESS_THAN(3,4,0)
            const PCType pc_type;
#else
            PCType pc_type;
#endif
            ierr = PCGetType ( M_pc, &pc_type );
            CHKERRABORT( this->worldComm().globalComm(),ierr );

            VLOG(2) << "preconditioner set as "  << pc_type << "\n";
        }
        else
        {
            this->setPetscPreconditionerType();
            // sets the software that is used to perform the factorization
            PetscPCFactorSetMatSolverPackage( M_pc,this->matSolverPackageType() );
        }

        if ( Environment::vm(_name="ksp-monitor",_prefix=this->prefix()).template as<bool>() )
        {
            KSPMonitorSet( M_ksp,KSPMonitorDefault,PETSC_NULL,PETSC_NULL );
        }

    }
}
コード例 #9
0
PetscErrorCode TSSetUp_Sundials_Nonlinear(TS ts)
{
  TS_Sundials    *cvode = (TS_Sundials*)ts->data;
  PetscErrorCode ierr;
  PetscInt       glosize,locsize,i,flag;
  PetscScalar    *y_data,*parray;
  void           *mem;
  const PCType   pctype;
  PetscTruth     pcnone;
  Vec            sol = ts->vec_sol;

  PetscFunctionBegin;
  ierr = PCSetFromOptions(cvode->pc);CHKERRQ(ierr);
  /* get the vector size */
  ierr = VecGetSize(ts->vec_sol,&glosize);CHKERRQ(ierr);
  ierr = VecGetLocalSize(ts->vec_sol,&locsize);CHKERRQ(ierr);

  /* allocate the memory for N_Vec y */
  cvode->y = N_VNew_Parallel(cvode->comm_sundials,locsize,glosize);
  if (!cvode->y) SETERRQ(1,"cvode->y is not allocated");

  /* initialize N_Vec y: copy ts->vec_sol to cvode->y */
  ierr = VecGetArray(ts->vec_sol,&parray);CHKERRQ(ierr);
  y_data = (PetscScalar *) N_VGetArrayPointer(cvode->y);
  for (i = 0; i < locsize; i++) y_data[i] = parray[i];
  /*ierr = PetscMemcpy(y_data,parray,locsize*sizeof(PETSC_SCALAR)); CHKERRQ(ierr);*/
  ierr = VecRestoreArray(ts->vec_sol,PETSC_NULL);CHKERRQ(ierr);
  ierr = VecDuplicate(ts->vec_sol,&cvode->update);CHKERRQ(ierr);  
  ierr = VecDuplicate(ts->vec_sol,&cvode->func);CHKERRQ(ierr);  
  ierr = PetscLogObjectParent(ts,cvode->update);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(ts,cvode->func);CHKERRQ(ierr);

  /* 
    Create work vectors for the TSPSolve_Sundials() routine. Note these are
    allocated with zero space arrays because the actual array space is provided 
    by Sundials and set using VecPlaceArray().
  */
  ierr = VecCreateMPIWithArray(((PetscObject)ts)->comm,locsize,PETSC_DECIDE,0,&cvode->w1);CHKERRQ(ierr);
  ierr = VecCreateMPIWithArray(((PetscObject)ts)->comm,locsize,PETSC_DECIDE,0,&cvode->w2);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(ts,cvode->w1);CHKERRQ(ierr);
  ierr = PetscLogObjectParent(ts,cvode->w2);CHKERRQ(ierr);

  /* Call CVodeCreate to create the solver memory and the use of a Newton iteration */
  mem = CVodeCreate(cvode->cvode_type, CV_NEWTON); 
  if (!mem) SETERRQ(PETSC_ERR_MEM,"CVodeCreate() fails");
  cvode->mem = mem;

  /* Set the pointer to user-defined data */
  flag = CVodeSetUserData(mem, ts);
  if (flag) SETERRQ(PETSC_ERR_LIB,"CVodeSetUserData() fails");

  /* Call CVodeInit to initialize the integrator memory and specify the
   * user's right hand side function in u'=f(t,u), the inital time T0, and
   * the initial dependent variable vector cvode->y */
  flag = CVodeInit(mem,TSFunction_Sundials,ts->ptime,cvode->y);
  if (flag){
    SETERRQ1(PETSC_ERR_LIB,"CVodeInit() fails, flag %d",flag);
  }

  flag = CVodeSStolerances(mem,cvode->reltol,cvode->abstol);
  if (flag){
    SETERRQ1(PETSC_ERR_LIB,"CVodeSStolerances() fails, flag %d",flag);
  }

  /* initialize the number of steps */
  ierr   = TSMonitor(ts,ts->steps,ts->ptime,sol);CHKERRQ(ierr); 

  /* call CVSpgmr to use GMRES as the linear solver.        */
  /* setup the ode integrator with the given preconditioner */
  ierr = PCGetType(cvode->pc,&pctype);CHKERRQ(ierr);
  ierr = PetscTypeCompare((PetscObject)cvode->pc,PCNONE,&pcnone);CHKERRQ(ierr);
  if (pcnone){
    flag  = CVSpgmr(mem,PREC_NONE,0);
    if (flag) SETERRQ1(PETSC_ERR_LIB,"CVSpgmr() fails, flag %d",flag);
  } else {
    flag  = CVSpgmr(mem,PREC_LEFT,0);
    if (flag) SETERRQ1(PETSC_ERR_LIB,"CVSpgmr() fails, flag %d",flag);

    /* Set preconditioner and solve routines Precond and PSolve, 
     and the pointer to the user-defined block data */
    flag = CVSpilsSetPreconditioner(mem,TSPrecond_Sundials,TSPSolve_Sundials);
    if (flag) SETERRQ1(PETSC_ERR_LIB,"CVSpilsSetPreconditioner() fails, flag %d", flag);
  }

  flag = CVSpilsSetGSType(mem, MODIFIED_GS);
  if (flag) SETERRQ1(PETSC_ERR_LIB,"CVSpgmrSetGSType() fails, flag %d",flag);
  PetscFunctionReturn(0);
}
コード例 #10
0
ファイル: parallel.c プロジェクト: kanika901/lighthouse
int main(int argc,char **args)
{
  Mat            A;        /* linear system matrix */
  PetscErrorCode ierr;
  PetscMPIInt    rank=0;
  PetscBool      flg;
  PetscViewer    fd;         /* viewer */
  PetscViewer    log;
  char           file[PETSC_MAX_PATH_LEN];
  char           logfile[PETSC_MAX_PATH_LEN];
  char           lockfile[PETSC_MAX_PATH_LEN], tmpstr[PETSC_MAX_PATH_LEN], dirname[PETSC_MAX_PATH_LEN], matrix[PETSC_MAX_PATH_LEN];
  char           hash[20];

  PetscLogDouble solveTime,endTime,startTime;
  PetscInt       its;
  PetscReal      norm;
  KSP            ksp; // Linear solver context
  Vec            b,x,u; // RHS, solution, vector for norm calculation
  PetscScalar    one = 1.0;
  PetscInt	 m, n, i;
  FILE           *lock;

/*
  if (rank == 0) {
    printf("Command line arguments:\n");
    for (i=0; i < argc; i++) 
      printf("%d: %s\n", i, args[i]);
  }
  // Save args
  int argcount = argc;
  char **argv = (char**) malloc (argc*sizeof(char*));
  for (i=0; i < argc; i++) {
    argv[i] = (char*) malloc(strlen(args[i]) + 1);
    strcpy(argv[i],args[i]);
  }
  MPI_Comm_rank(MPI_COMM_WORLD,&rank);
*/
  PetscInitialize(&argc,&args,(char *)0,help);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  ierr = PetscOptionsGetString(PETSC_NULL,"-hash",hash,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
  if (!flg) {
    strcpy(hash,"nohash");
  }

  ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
  if (!flg) {
    PetscPrintf(PETSC_COMM_WORLD,"Must indicate matrix file with the -f option");
  }
  /* Create lock file */
  if (rank == 0) {
    for (i = strlen(file); i> 0; i--) if (file[i] == '.') break;
    strncpy(tmpstr, file, i-1);
    for (i = strlen(tmpstr); i> 0; i--) if (file[i] == '/') break;
    strncpy(dirname, tmpstr, i);
    dirname[i] = '\0';
    sprintf(lockfile,"%s/../timing/.%s.%s", dirname, basename(tmpstr), hash);
    sprintf(logfile,"%s/../timing/%s.%s.log", dirname, basename(tmpstr), hash);
    lock =  fopen(lockfile, "w");
    fprintf(lock, "%s\n", file);
    fclose(lock);
  }
  /* Read file */
  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
  // Create matrix
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetType(A,MATMPIAIJ); CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  // Load matrix from file
  ierr = MatLoad(A,fd);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
  ierr = MatGetSize(A, &m, &n); CHKERRQ(ierr);
  // Assemble matrix
  //ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  //ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  // Create RHS vector
  ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
  ierr = VecSetSizes(b,PETSC_DECIDE,n); CHKERRQ(ierr);
  ierr = VecSetFromOptions(b);CHKERRQ(ierr);
  ierr = VecSet(b,one);  CHKERRQ(ierr);
  //ierr = VecLoad(b,fd);CHKERRQ(ierr);
  // Create vectors x and u
  ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
  ierr = VecDuplicate(b,&u);CHKERRQ(ierr);

  // Create KSP
  ierr = KSPCreate(PETSC_COMM_WORLD,&ksp); CHKERRQ(ierr);
  ierr = KSPSetInitialGuessNonzero(ksp,PETSC_FALSE);CHKERRQ(ierr);
  ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr);
  ierr = KSPSetFromOptions(ksp); CHKERRQ(ierr);
  // Setup KSP
  ierr = KSPSetUp(ksp);CHKERRQ(ierr);
  ierr = KSPSetUpOnBlocks(ksp);CHKERRQ(ierr);
  // Get start time
  ierr = PetscTime(&startTime);CHKERRQ(ierr);
  // Get KSP and PC type
  KSPType kt;
  ierr = KSPGetType(ksp,&kt);
  PC pc;
  ierr = KSPGetPC(ksp,&pc);
  PCType pt;
  ierr = PCGetType(pc,&pt);
  // Print method info
  ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD, logfile, &log); CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(log, "Hash: %s\n", hash);
  ierr = PetscViewerASCIIPrintf(log, "%s | %s",kt,pt);CHKERRQ(ierr);
  // Make sure the program doesn't crash 
  // while trying to solve the system
  PetscPushErrorHandler(PetscIgnoreErrorHandler,NULL);
  ierr = KSPSolve(ksp,b,x);
  PetscPopErrorHandler();
  // Check if anything went wrong
  if(ierr == 0 || ierr == -1){ 
    // If no error occurred or stopped by MyKSPMonitor, 
    // compute normal and stuff
    ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
    ierr = MatMult(A,x,u);CHKERRQ(ierr);
    ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr);
    ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
    ierr = PetscTime(&endTime);CHKERRQ(ierr);
    // Compute solve time
    solveTime = endTime - startTime;
    // Check if KSP converged
    KSPConvergedReason reason;
    KSPGetConvergedReason(ksp,&reason);
    // Print convergence code, solve time, preconditioned norm, iterations
    ierr = PetscViewerASCIIPrintf(log, " | %D | %e | %g | %D\n",reason,solveTime,norm,its);CHKERRQ(ierr);
    ierr = KSPView(ksp,log);
    ierr = PCView(pc,log);
    ierr = PetscLogView(log);
  }
  else{
    // Disaster happened, bail out
    if (rank == 0) remove(lockfile);
    PetscFinalize();
    return 0;
  }
  // Again, destroy KSP and vector
  ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = VecDestroy(&b);CHKERRQ(ierr);
  ierr = VecDestroy(&u);CHKERRQ(ierr);  

  if (rank == 0) remove(lockfile);
  PetscFinalize();
  return 0;
}
コード例 #11
0
ファイル: ex2.c プロジェクト: masa-ito/PETScToPoisson
int main(int argc,char **args)
{
  Mat            mat;          /* matrix */
  Vec            b,ustar,u;  /* vectors (RHS, exact solution, approx solution) */
  PC             pc;           /* PC context */
  KSP            ksp;          /* KSP context */
  PetscErrorCode ierr;
  PetscInt       n = 10,i,its,col[3];
  PetscScalar    value[3];
  PCType         pcname;
  KSPType        kspname;
  PetscReal      norm,tol=1000.*PETSC_MACHINE_EPSILON;

  PetscInitialize(&argc,&args,(char*)0,help);

  /* Create and initialize vectors */
  ierr = VecCreateSeq(PETSC_COMM_SELF,n,&b);CHKERRQ(ierr);
  ierr = VecCreateSeq(PETSC_COMM_SELF,n,&ustar);CHKERRQ(ierr);
  ierr = VecCreateSeq(PETSC_COMM_SELF,n,&u);CHKERRQ(ierr);
  ierr = VecSet(ustar,1.0);CHKERRQ(ierr);
  ierr = VecSet(u,0.0);CHKERRQ(ierr);

  /* Create and assemble matrix */
  ierr     = MatCreateSeqAIJ(PETSC_COMM_SELF,n,n,3,NULL,&mat);CHKERRQ(ierr);
  value[0] = -1.0; value[1] = 2.0; value[2] = -1.0;
  for (i=1; i<n-1; i++) {
    col[0] = i-1; col[1] = i; col[2] = i+1;
    ierr   = MatSetValues(mat,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
  }
  i    = n - 1; col[0] = n - 2; col[1] = n - 1;
  ierr = MatSetValues(mat,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
  i    = 0; col[0] = 0; col[1] = 1; value[0] = 2.0; value[1] = -1.0;
  ierr = MatSetValues(mat,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  /* Compute right-hand-side vector */
  ierr = MatMult(mat,ustar,b);CHKERRQ(ierr);

  /* Create PC context and set up data structures */
  ierr = PCCreate(PETSC_COMM_WORLD,&pc);CHKERRQ(ierr);
  ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
  ierr = PCSetFromOptions(pc);CHKERRQ(ierr);
  ierr = PCSetOperators(pc,mat,mat);CHKERRQ(ierr);
  ierr = PCSetUp(pc);CHKERRQ(ierr);

  /* Create KSP context and set up data structures */
  ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
  ierr = KSPSetType(ksp,KSPRICHARDSON);CHKERRQ(ierr);
  ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
  ierr = PCSetOperators(pc,mat,mat);CHKERRQ(ierr);
  ierr = KSPSetPC(ksp,pc);CHKERRQ(ierr);
  ierr = KSPSetUp(ksp);CHKERRQ(ierr);

  /* Solve the problem */
  ierr = KSPGetType(ksp,&kspname);CHKERRQ(ierr);
  ierr = PCGetType(pc,&pcname);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_SELF,"Running %s with %s preconditioning\n",kspname,pcname);CHKERRQ(ierr);
  ierr = KSPSolve(ksp,b,u);CHKERRQ(ierr);
  ierr = VecAXPY(u,-1.0,ustar);CHKERRQ(ierr);
  ierr = VecNorm(u,NORM_2,&norm);
  ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
  if (norm > tol) {
    ierr = PetscPrintf(PETSC_COMM_SELF,"2 norm of error %g Number of iterations %D\n",(double)norm,its);CHKERRQ(ierr);
  }

  /* Free data structures */
  ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
  ierr = VecDestroy(&u);CHKERRQ(ierr);
  ierr = VecDestroy(&ustar);CHKERRQ(ierr);
  ierr = VecDestroy(&b);CHKERRQ(ierr);
  ierr = MatDestroy(&mat);CHKERRQ(ierr);
  ierr = PCDestroy(&pc);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return 0;
}
コード例 #12
0
int main(int argc, char *argv[])
{
	// Initialize libMesh
	libMesh::LibMeshInit init(argc, argv);
	libMesh::Parallel::Communicator& WorldComm = init.comm();

    libMesh::PetscMatrix<libMesh::Number> matrix_A(WorldComm);
    matrix_A.init(4,4,4,4);

    matrix_A.set(0,0,1.);
//    matrix_A.set(0,1,2.);
//    matrix_A.set(0,2,3.);
//    matrix_A.set(0,3,4.);

//    matrix_A.set(1,0,2.);
    matrix_A.set(1,1,5.);
//    matrix_A.set(1,2,3.);
//    matrix_A.set(1,3,7.);

//    matrix_A.set(2,0,3.);
//    matrix_A.set(2,1,3.);
    matrix_A.set(2,2,9.);
//    matrix_A.set(2,3,6.);

//    matrix_A.set(3,0,4.);
//    matrix_A.set(3,1,7.);
//    matrix_A.set(3,2,6.);
    matrix_A.set(3,3,1.);

    matrix_A.close();

    Mat dummy_inv_A;
    MatCreate(PETSC_COMM_WORLD,&dummy_inv_A);
    MatSetType(dummy_inv_A,MATMPIAIJ);
    MatSetSizes(dummy_inv_A,PETSC_DECIDE,PETSC_DECIDE,4,4);
    MatMPIAIJSetPreallocation(dummy_inv_A,2,NULL,0,NULL);
    MatSetUp(dummy_inv_A);

    // Dummy matrices
//    Mat dummy_A, dummy_inv_A;
//
//
    libMesh::PetscVector<libMesh::Number> vector_unity(WorldComm,4,4);
    libMesh::PetscVector<libMesh::Number> vector_dummy_answer(WorldComm,4,4);

	VecSet(vector_unity.vec(),1);
	vector_unity.close();

	VecSet(vector_dummy_answer.vec(),0);
	vector_dummy_answer.close();

    // Solver
//	libMesh::PetscLinearSolver<libMesh::Number> KSP_dummy_solver(WorldComm);
//	KSP_dummy_solver.init(&matrix_A);

//	KSPSetOperators(KSP_dummy_solver.ksp(),matrix_A.mat(),NULL);

	KSP ksp;
	PC pc;

	KSPCreate(PETSC_COMM_WORLD,&ksp);
	KSPSetOperators(ksp, matrix_A.mat(), matrix_A.mat());
	KSPGetPC(ksp,&pc);
	PCSetFromOptions(pc);
	PCType dummy_type;
	PCGetType(pc,&dummy_type);
	std::cout << std::endl << dummy_type << std::endl << std::endl;
//	PCSetType(pc,PCSPAI);
//	PCHYPRESetType(pc,"parasails");
	KSPSetUp(ksp);
	KSPSolve(ksp,vector_unity.vec(),vector_dummy_answer.vec());
	PCComputeExplicitOperator(pc,&dummy_inv_A);
//	KSPGetOperators(KSP_dummy_solver.ksp(),&dummy_A,&dummy_inv_A);

	libMesh::PetscMatrix<libMesh::Number> matrix_invA(dummy_inv_A,WorldComm);
	matrix_invA.close();
//
//	//    KSP_dummy_solver.solve(matrix_A,vector_dummy_answer,vector_unity,1E-5,10000);
//
//	vector_dummy_answer.print_matlab();
//

//	libMesh::PetscMatrix<libMesh::Number> product_mat(WorldComm);
	matrix_A.print_matlab();
	matrix_invA.print_matlab();
	vector_dummy_answer.print_matlab();
	return 0;
}
コード例 #13
0
ファイル: PETScLinearSolver.cpp プロジェクト: drjod/ogs_kb1
void PETScLinearSolver::Solver()
{
  
   //TEST
#ifdef TEST_MEM_PETSC
   PetscLogDouble mem1, mem2;
   PetscMemoryGetCurrentUsage(&mem1);
#endif
 
  /* 
  //TEST
  PetscViewer viewer;
  PetscViewerASCIIOpen(PETSC_COMM_WORLD, "x.txt", &viewer);
  PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_MATLAB);
  PetscObjectSetName((PetscObject)x,"Solution");
  VecView(x, viewer);   
  */


   int its; 
   PetscLogDouble v1,v2;
   KSPConvergedReason reason;

   // #define PETSC34
   //kg44 quick fix to compile PETSC with version PETSCV3.4
#ifdef USEPETSC34
   PetscTime(&v1);
#else
   PetscGetTime(&v1);
#endif

#if (PETSC_VERSION_MAJOR == 3) && (PETSC_VERSION_MINOR > 4)
   KSPSetOperators(lsolver, A, A);
#else
   KSPSetOperators(lsolver, A, A, DIFFERENT_NONZERO_PATTERN);
#endif

   KSPSolve(lsolver, b, x);
  
   KSPGetConvergedReason(lsolver,&reason); //CHKERRQ(ierr);
   if (reason==KSP_DIVERGED_INDEFINITE_PC)
   {
     PetscPrintf(PETSC_COMM_WORLD,"\nDivergence because of indefinite preconditioner;\n");
     PetscPrintf(PETSC_COMM_WORLD,"Run the executable again but with -pc_factor_shift_positive_definite option.\n");
   }
   else if (reason<0)
   {
     PetscPrintf(PETSC_COMM_WORLD,"\nOther kind of divergence: this should not happen.\n");
   }
   else 
   {
     const char *slv_type;
     const char *prc_type;
     KSPGetType(lsolver, &slv_type);
     PCGetType(prec, &prc_type);

      PetscPrintf(PETSC_COMM_WORLD,"\n================================================");         
      PetscPrintf(PETSC_COMM_WORLD, "\nLinear solver %s with %s preconditioner",
                                    slv_type, prc_type);         
      KSPGetIterationNumber(lsolver,&its); //CHKERRQ(ierr);
      PetscPrintf(PETSC_COMM_WORLD,"\nConvergence in %d iterations.\n",(int)its);
      PetscPrintf(PETSC_COMM_WORLD,"\n================================================");           
   }
   PetscPrintf(PETSC_COMM_WORLD,"\n");

   //VecAssemblyBegin(x);
   //VecAssemblyEnd(x);

   //kg44 quick fix to compile PETSC with version PETSCV3.4
#ifdef USEPETSC34
   PetscTime(&v2);
#else
   PetscGetTime(&v2);
#endif

   time_elapsed += v2-v1;

   
#define aTEST_OUT
#ifdef TEST_OUT
  //TEST
   PetscViewer viewer;
   PetscViewerASCIIOpen(PETSC_COMM_WORLD, "x2.txt", &viewer);
   PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_MATLAB);
   PetscObjectSetName((PetscObject)A,"Matrix");
   MatView(A, viewer);
   PetscObjectSetName((PetscObject)x,"Solution");
   VecView(x, viewer);
   PetscObjectSetName((PetscObject)b,"RHS");
   VecView(b, viewer);   
    VecDestroy(&b);
  VecDestroy(&x);
  MatDestroy(&A);
  if(lsolver) KSPDestroy(&lsolver);
  // if(prec) PCDestroy(&prec);
  if(global_x0)
    delete []  global_x0;
  if(global_x1)
    delete []  global_x1;
   PetscFinalize();
   exit(0);
#endif


#ifdef TEST_MEM_PETSC
  //TEST
   PetscMemoryGetCurrentUsage(&mem2);
   PetscPrintf(PETSC_COMM_WORLD, "###Memory usage by solver. Before :%f After:%f Increase:%d\n", mem1, mem2, (int)(mem2 - mem1));
#endif
}
コード例 #14
0
std::pair<std::string,std::string>
RBConstructionBase<Base>::set_alternative_solver
(AutoPtr<LinearSolver<Number> >&
#ifdef LIBMESH_HAVE_PETSC
 ls
#endif
 )
{
  // It seems that setting it this generic way has no effect...
  // PreconditionerType orig_pc = this->linear_solver->preconditioner_type();
  // this->linear_solver->set_preconditioner_type(AMG_PRECOND);
  // so we do it the "hard" way.
  std::string orig_petsc_pc_type_string, orig_petsc_ksp_type_string;

#ifdef LIBMESH_HAVE_PETSC
  // ... but we can set it the "hard" way
  PetscLinearSolver<Number>* petsc_linear_solver =
    libmesh_cast_ptr<PetscLinearSolver<Number>*>(ls.get());

  // Note: #define PCType char*, and PCGetType just sets a pointer.  We'll use
  // the string below to make a real copy, and set the PC back to its original
  // type at the end of the function.
#if PETSC_VERSION_LESS_THAN(3,0,0) || !PETSC_VERSION_LESS_THAN(3,4,0)
  // Pre-3.0 and petsc-dev (as of October 2012) use non-const versions
  PCType orig_petsc_pc_type;
  KSPType orig_petsc_ksp_type;
#else
  const PCType orig_petsc_pc_type;
  const KSPType orig_petsc_ksp_type;
#endif

  if (petsc_linear_solver)
    {
      PC pc = petsc_linear_solver->pc();
      int ierr = PCGetType(pc, &orig_petsc_pc_type);
      LIBMESH_CHKERRABORT(ierr);

      KSP ksp = petsc_linear_solver->ksp();
      ierr = KSPGetType(ksp, &orig_petsc_ksp_type);
      LIBMESH_CHKERRABORT(ierr);

      // libMesh::out << "orig_petsc_pc_type (before)=" << orig_petsc_pc_type << std::endl;
      // Make actual copies of the original PC and KSP types
      orig_petsc_pc_type_string = orig_petsc_pc_type;
      orig_petsc_ksp_type_string = orig_petsc_ksp_type;

#ifdef LIBMESH_HAVE_PETSC_HYPRE
      // Set solver/PC combo specified in input file...
      if (this->alternative_solver == "amg")
        {
          // Set HYPRE and boomeramg PC types
          ierr = PCSetType(pc, PCHYPRE);
          LIBMESH_CHKERRABORT(ierr);
          ierr = PCHYPRESetType(pc, "boomeramg");
          LIBMESH_CHKERRABORT(ierr);
        }
#endif // LIBMESH_HAVE_PETSC_HYPRE
      if (this->alternative_solver == "mumps")
        {
          // We'll use MUMPS... TODO: configure libmesh to detect
          // when MUMPS is available via PETSc.

          // No initial guesses can be specified with KSPPREONLY.  We
          // can leave the solver as gmres or whatever and it should
          // converge in 1 iteration.  Otherwise, to use KSPPREONLY,
          // you may need to do:
          // KSPSetInitialGuessNonzero(ksp, PETSC_FALSE);
          // ierr = KSPSetType(ksp, KSPPREONLY);
          // LIBMESH_CHKERRABORT(ierr);

          // Need to call the equivalent for the command line options:
          // -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package mumps
          ierr = PCSetType(pc, PCLU);
          LIBMESH_CHKERRABORT(ierr);
#if !(PETSC_VERSION_LESS_THAN(3,0,0))
          ierr = PCFactorSetMatSolverPackage(pc,"mumps");
          LIBMESH_CHKERRABORT(ierr);
#endif
        }
    }
  else
    {
      // Otherwise, the cast failed and we are not using PETSc...
      libMesh::out << "You are not using PETSc, so don't know how to set AMG PC." << std::endl;
      libMesh::out << "Returning empty string!" << std::endl;
    }
#endif // LIBMESH_HAVE_PETSC

  return std::make_pair(orig_petsc_pc_type_string, orig_petsc_ksp_type_string);
}
コード例 #15
0
ファイル: bddcschurs.c プロジェクト: PeiLiu90/petsc
PetscErrorCode PCBDDCSubSchursSetUp(PCBDDCSubSchurs sub_schurs, Mat S, IS is_A_I, IS is_A_B, PetscInt ncc, IS is_cc[], PetscInt xadj[], PetscInt adjncy[], PetscInt nlayers)
{
  Mat                    A_II,A_IB,A_BI,A_BB;
  ISLocalToGlobalMapping BtoNmap,ItoNmap;
  PetscBT                touched;
  PetscInt               i,n_I,n_B,n_local,*local_numbering;
  PetscBool              is_sorted;
  PetscErrorCode         ierr;

  PetscFunctionBegin;
  ierr = ISSorted(is_A_I,&is_sorted);CHKERRQ(ierr);
  if (!is_sorted) {
    SETERRQ(PetscObjectComm((PetscObject)is_A_I),PETSC_ERR_PLIB,"IS for I dofs should be shorted");
  }
  ierr = ISSorted(is_A_B,&is_sorted);CHKERRQ(ierr);
  if (!is_sorted) {
    SETERRQ(PetscObjectComm((PetscObject)is_A_B),PETSC_ERR_PLIB,"IS for B dofs should be shorted");
  }

  /* get sizes */
  ierr = ISGetLocalSize(is_A_I,&n_I);CHKERRQ(ierr);
  ierr = ISGetLocalSize(is_A_B,&n_B);CHKERRQ(ierr);
  n_local = n_I+n_B;

  /* maps */
  ierr = ISLocalToGlobalMappingCreateIS(is_A_B,&BtoNmap);CHKERRQ(ierr);
  if (nlayers >= 0 && xadj != NULL && adjncy != NULL) { /* I problems have a different size of the original ones */
    ierr = ISLocalToGlobalMappingCreateIS(is_A_I,&ItoNmap);CHKERRQ(ierr);
    /* allocate some auxiliary space */
    ierr = PetscMalloc1(n_local,&local_numbering);CHKERRQ(ierr);
    ierr = PetscBTCreate(n_local,&touched);CHKERRQ(ierr);
  } else {
    ItoNmap = 0;
    local_numbering = 0;
    touched = 0;
  }

  /* get Schur complement matrices */
  ierr = MatSchurComplementGetSubMatrices(S,&A_II,NULL,&A_IB,&A_BI,&A_BB);CHKERRQ(ierr);

  /* allocate space for schur complements */
  ierr = PetscMalloc5(ncc,&sub_schurs->is_AEj_I,ncc,&sub_schurs->is_AEj_B,ncc,&sub_schurs->S_Ej,ncc,&sub_schurs->work1,ncc,&sub_schurs->work2);CHKERRQ(ierr);
  sub_schurs->n_subs = ncc;

  /* cycle on subsets and extract schur complements */
  for (i=0;i<sub_schurs->n_subs;i++) {
    Mat      AE_II,AE_IE,AE_EI,AE_EE;
    IS       is_I,is_subset_B;

    /* get IS for subsets in B numbering */
    ierr = ISDuplicate(is_cc[i],&sub_schurs->is_AEj_B[i]);CHKERRQ(ierr);
    ierr = ISSort(sub_schurs->is_AEj_B[i]);CHKERRQ(ierr);
    ierr = ISGlobalToLocalMappingApplyIS(BtoNmap,IS_GTOLM_DROP,sub_schurs->is_AEj_B[i],&is_subset_B);CHKERRQ(ierr);

    /* BB block on subset */
    ierr = MatGetSubMatrix(A_BB,is_subset_B,is_subset_B,MAT_INITIAL_MATRIX,&AE_EE);CHKERRQ(ierr);

    if (ItoNmap) { /* is ItoNmap has been computed, extracts only a part of I dofs */
      const PetscInt* idx_B;
      PetscInt        n_local_dofs,n_prev_added,j,layer,subset_size;

      /* all boundary dofs must be skipped when adding layers */
      ierr = PetscBTMemzero(n_local,touched);CHKERRQ(ierr);
      ierr = ISGetIndices(is_A_B,&idx_B);CHKERRQ(ierr);
      for (j=0;j<n_B;j++) {
        ierr = PetscBTSet(touched,idx_B[j]);CHKERRQ(ierr);
      }
      ierr = ISRestoreIndices(is_A_B,&idx_B);CHKERRQ(ierr);

      /* add next layers of dofs */
      ierr = ISGetLocalSize(is_cc[i],&subset_size);CHKERRQ(ierr);
      ierr = ISGetIndices(is_cc[i],&idx_B);CHKERRQ(ierr);
      ierr = PetscMemcpy(local_numbering,idx_B,subset_size*sizeof(PetscInt));CHKERRQ(ierr);
      ierr = ISRestoreIndices(is_cc[i],&idx_B);CHKERRQ(ierr);
      n_local_dofs = subset_size;
      n_prev_added = subset_size;
      for (layer=0;layer<nlayers;layer++) {
        PetscInt n_added;
        if (n_local_dofs == n_I+subset_size) break;
        if (n_local_dofs > n_I+subset_size) {
          SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Error querying layer %d. Out of bound access (%d > %d)",layer,n_local_dofs,n_I+subset_size);
        }
        ierr = PCBDDCAdjGetNextLayer_Private(local_numbering+n_local_dofs,n_prev_added,touched,xadj,adjncy,&n_added);CHKERRQ(ierr);
        n_prev_added = n_added;
        n_local_dofs += n_added;
        if (!n_added) break;
      }

      /* IS for I dofs in original numbering and in I numbering */
      ierr = ISCreateGeneral(PetscObjectComm((PetscObject)ItoNmap),n_local_dofs-subset_size,local_numbering+subset_size,PETSC_COPY_VALUES,&sub_schurs->is_AEj_I[i]);CHKERRQ(ierr);
      ierr = ISSort(sub_schurs->is_AEj_I[i]);CHKERRQ(ierr);
      ierr = ISGlobalToLocalMappingApplyIS(ItoNmap,IS_GTOLM_DROP,sub_schurs->is_AEj_I[i],&is_I);CHKERRQ(ierr);

      /* II block */
      ierr = MatGetSubMatrix(A_II,is_I,is_I,MAT_INITIAL_MATRIX,&AE_II);CHKERRQ(ierr);
    } else { /* in this case we can take references of already existing IS and matrices for I dofs */
      /* IS for I dofs in original numbering */
      ierr = PetscObjectReference((PetscObject)is_A_I);CHKERRQ(ierr);
      sub_schurs->is_AEj_I[i] = is_A_I;

      /* IS for I dofs in I numbering TODO: "first" argument of ISCreateStride is not general */
      ierr = ISCreateStride(PetscObjectComm((PetscObject)is_A_I),n_I,0,1,&is_I);CHKERRQ(ierr);

      /* II block is the same */
      ierr = PetscObjectReference((PetscObject)A_II);CHKERRQ(ierr);
      AE_II = A_II;
    }

    /* IE block */
    ierr = MatGetSubMatrix(A_IB,is_I,is_subset_B,MAT_INITIAL_MATRIX,&AE_IE);CHKERRQ(ierr);

    /* EI block */
    ierr = MatGetSubMatrix(A_BI,is_subset_B,is_I,MAT_INITIAL_MATRIX,&AE_EI);CHKERRQ(ierr);

    /* setup Schur complements on subset */
    ierr = MatCreateSchurComplement(AE_II,AE_II,AE_IE,AE_EI,AE_EE,&sub_schurs->S_Ej[i]);CHKERRQ(ierr);
    ierr = MatGetVecs(sub_schurs->S_Ej[i],&sub_schurs->work1[i],&sub_schurs->work2[i]);CHKERRQ(ierr);
    if (AE_II == A_II) { /* we can reuse the same ksp */
      KSP ksp;
      ierr = MatSchurComplementGetKSP(S,&ksp);CHKERRQ(ierr);
      ierr = MatSchurComplementSetKSP(sub_schurs->S_Ej[i],ksp);CHKERRQ(ierr);
    } else { /* build new ksp object which inherits ksp and pc types from the original one */
      KSP      origksp,schurksp;
      PC       origpc,schurpc;
      KSPType  ksp_type;
      PCType   pc_type;
      PetscInt n_internal;

      ierr = MatSchurComplementGetKSP(S,&origksp);CHKERRQ(ierr);
      ierr = MatSchurComplementGetKSP(sub_schurs->S_Ej[i],&schurksp);CHKERRQ(ierr);
      ierr = KSPGetType(origksp,&ksp_type);CHKERRQ(ierr);
      ierr = KSPSetType(schurksp,ksp_type);CHKERRQ(ierr);
      ierr = KSPGetPC(schurksp,&schurpc);CHKERRQ(ierr);
      ierr = KSPGetPC(origksp,&origpc);CHKERRQ(ierr);
      ierr = PCGetType(origpc,&pc_type);CHKERRQ(ierr);
      ierr = PCSetType(schurpc,pc_type);CHKERRQ(ierr);
      ierr = ISGetSize(is_I,&n_internal);CHKERRQ(ierr);
      if (n_internal) { /* UMFPACK gives error with 0 sized problems */
        MatSolverPackage solver=NULL;
        ierr = PCFactorGetMatSolverPackage(origpc,(const MatSolverPackage*)&solver);CHKERRQ(ierr);
        if (solver) {
          ierr = PCFactorSetMatSolverPackage(schurpc,solver);CHKERRQ(ierr);
        }
      }
      ierr = KSPSetUp(schurksp);CHKERRQ(ierr);
    }
    /* free */
    ierr = MatDestroy(&AE_II);CHKERRQ(ierr);
    ierr = MatDestroy(&AE_EE);CHKERRQ(ierr);
    ierr = MatDestroy(&AE_IE);CHKERRQ(ierr);
    ierr = MatDestroy(&AE_EI);CHKERRQ(ierr);
    ierr = ISDestroy(&is_I);CHKERRQ(ierr);
    ierr = ISDestroy(&is_subset_B);CHKERRQ(ierr);
  }
  /* free */
  ierr = ISLocalToGlobalMappingDestroy(&ItoNmap);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingDestroy(&BtoNmap);CHKERRQ(ierr);
  ierr = PetscFree(local_numbering);CHKERRQ(ierr);
  ierr = PetscBTDestroy(&touched);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
コード例 #16
0
ファイル: ef_solver.c プロジェクト: tuxfan/ska
PetscErrorCode efs_setup(efs *slv, int offset[], int stride[])
{
	PetscErrorCode ierr;
	PetscInt xs, ys, zs, xm, ym, zm;
	PCType pc_type;

	if (efs_log(slv, EFS_LOG_STATUS)) {
		ierr = ef_io_print(slv->comm, "Setting up electric field solver");CHKERRQ(ierr);
	}

	slv->ts = 0;

	if (efs_log(slv, EFS_LOG_RESIDUAL)) {
		ierr = PetscOptionsSetValue("-ksp_monitor_short", NULL);CHKERRQ(ierr);
	}

	ierr = DMDASetFieldName(slv->dm, 0,"potential");CHKERRQ(ierr);

	if (slv->grid.nd == 2) {
		ierr = DMDAGetCorners(slv->dm, &xs, &ys, 0, &xm, &ym, 0);CHKERRQ(ierr);
		slv->dmap = ef_dmap_create_2d(xs - offset[0], ys - offset[1], xm, ym, stride);
	} else if (slv->grid.nd == 3) {
		ierr = DMDAGetCorners(slv->dm, &xs, &ys, &zs, &xm, &ym, &zm);CHKERRQ(ierr);
		slv->dmap = ef_dmap_create_3d(xs - offset[0], ys - offset[1], zs - offset[2], xm, ym, zm, stride);
	} else {
		SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_SUP, "Unsupported dimmension: %d", slv->grid.nd);
	}
	ierr = ef_callback_create(&slv->callback);CHKERRQ(ierr);

	ierr = KSPCreate(slv->comm, &slv->ksp);CHKERRQ(ierr);
	if (efs_log(slv, EFS_LOG_EIGS)) {
		ierr = KSPSetComputeEigenvalues(slv->ksp, PETSC_TRUE);CHKERRQ(ierr);
	}
	ierr = KSPSetDM(slv->ksp, slv->dm);CHKERRQ(ierr);
	ierr = KSPGetPC(slv->ksp, &slv->pc);CHKERRQ(ierr);
	ierr = PCSetType(slv->pc, PCMG);CHKERRQ(ierr);
	if (slv->options.galerkin) {
		ierr = PCMGSetGalerkin(slv->pc, PETSC_TRUE);CHKERRQ(ierr);
	} else {
		ierr = PCMGSetGalerkin(slv->pc, PETSC_FALSE);CHKERRQ(ierr);
	}

	ierr = KSPSetComputeOperators(slv->ksp, slv->callback->matrix, slv);CHKERRQ(ierr);
	ierr = KSPSetComputeRHS(slv->ksp, slv->callback->rhs, slv);CHKERRQ(ierr);
	ierr = KSPSetComputeInitialGuess(slv->ksp, slv->callback->guess, slv);CHKERRQ(ierr);
	ierr = KSPSetFromOptions(slv->ksp);CHKERRQ(ierr);

	ierr = PCGetType(slv->pc, &pc_type);CHKERRQ(ierr);

	ierr = PCMGGetLevels(slv->pc, &slv->options.levels);CHKERRQ(ierr);
	if (slv->options.levels < 1) slv->options.levels++;
	ierr = PCMGGetGalerkin(slv->pc, &slv->options.galerkin);CHKERRQ(ierr);
	if (strcmp(pc_type, PCGAMG) == 0
	    || strcmp(pc_type, PCHYPRE) == 0) slv->options.galerkin = 1;
	if (!slv->options.galerkin) {
		slv->levels = (ef_level*) malloc(slv->options.levels*sizeof(ef_level));
		// setup callback for transforming rhs on coarse levels
	} else {
		slv->levels = (ef_level*) malloc(sizeof(ef_level));
	}
	ierr = ef_fd_create(&slv->fd, EF_FD_STANDARD_O2);CHKERRQ(ierr);
	ierr = ef_operator_create(&slv->op, slv->levels, slv->fd, slv->grid.nd);CHKERRQ(ierr);
	ierr = ef_boundary_create(&slv->boundary, slv->levels, slv->options.levels,
	                          slv->dmap, &slv->state, slv->fd);CHKERRQ(ierr);
	slv->op->axisymmetric = slv->options.axisymmetric;
	slv->boundary->axisymmetric = slv->options.axisymmetric;
	ierr = DMSetMatType(slv->dm, MATAIJ);CHKERRQ(ierr);
	ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].eps);CHKERRQ(ierr);
	ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].g);CHKERRQ(ierr);
	ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].ag);CHKERRQ(ierr);
	ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].gcomp);CHKERRQ(ierr);
	ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].scale);CHKERRQ(ierr);
	ierr = DMCreateGlobalVector(slv->dm, &slv->levels[0].nscale);CHKERRQ(ierr);
	ierr = VecSet(slv->levels[0].g, 0);CHKERRQ(ierr);
	ierr = VecSet(slv->levels[0].gcomp, 1);CHKERRQ(ierr);
	ierr = VecSet(slv->levels[0].scale, 1);CHKERRQ(ierr);
	ierr = VecSet(slv->levels[0].nscale, 1);CHKERRQ(ierr);

	ierr = DMCoarsenHookAdd(slv->dm, slv->callback->coarsen, slv->callback->restrct, slv);CHKERRQ(ierr);

	return 0;
}
コード例 #17
0
ファイル: PETScLinearSolver.cpp プロジェクト: TomFischer/ogs
bool PETScLinearSolver::solve(PETScMatrix& A, PETScVector& b, PETScVector& x)
{
    BaseLib::RunTime wtimer;
    wtimer.start();

// define TEST_MEM_PETSC
#ifdef TEST_MEM_PETSC
    PetscLogDouble mem1, mem2;
    PetscMemoryGetCurrentUsage(&mem1);
#endif

#if (PETSC_VERSION_NUMBER > 3040)
    KSPSetOperators(_solver, A.getRawMatrix(), A.getRawMatrix());
#else
    KSPSetOperators(_solver, A.getRawMatrix(), A.getRawMatrix(),
                    DIFFERENT_NONZERO_PATTERN);
#endif

    KSPSolve(_solver, b.getRawVector(), x.getRawVector());

    KSPConvergedReason reason;
    KSPGetConvergedReason(_solver, &reason);

    bool converged = true;
    if (reason > 0)
    {
        const char* ksp_type;
        const char* pc_type;
        KSPGetType(_solver, &ksp_type);
        PCGetType(_pc, &pc_type);

        PetscPrintf(PETSC_COMM_WORLD,
                    "\n================================================");
        PetscPrintf(PETSC_COMM_WORLD,
                    "\nLinear solver %s with %s preconditioner", ksp_type,
                    pc_type);

        PetscInt its;
        KSPGetIterationNumber(_solver, &its);
        PetscPrintf(PETSC_COMM_WORLD, "\nconverged in %d iterations", its);
        switch (reason)
        {
            case KSP_CONVERGED_RTOL:
                PetscPrintf(PETSC_COMM_WORLD,
                            " (relative convergence criterion fulfilled).");
                break;
            case KSP_CONVERGED_ATOL:
                PetscPrintf(PETSC_COMM_WORLD,
                            " (absolute convergence criterion fulfilled).");
                break;
            default:
                PetscPrintf(PETSC_COMM_WORLD, ".");
        }

        PetscPrintf(PETSC_COMM_WORLD,
                    "\n================================================\n");
    }
    else if (reason == KSP_DIVERGED_ITS)
    {
        const char* ksp_type;
        const char* pc_type;
        KSPGetType(_solver, &ksp_type);
        PCGetType(_pc, &pc_type);
        PetscPrintf(PETSC_COMM_WORLD,
                    "\nLinear solver %s with %s preconditioner", ksp_type,
                    pc_type);
        PetscPrintf(PETSC_COMM_WORLD,
                    "\nWarning: maximum number of iterations reached.\n");
    }
    else
    {
        converged = false;
        if (reason == KSP_DIVERGED_INDEFINITE_PC)
        {
            PetscPrintf(PETSC_COMM_WORLD,
                        "\nDivergence because of indefinite preconditioner,");
            PetscPrintf(PETSC_COMM_WORLD,
                        "\nTry to run again with "
                        "-pc_factor_shift_positive_definite option.\n");
        }
        else if (reason == KSP_DIVERGED_BREAKDOWN_BICG)
        {
            PetscPrintf(PETSC_COMM_WORLD,
                        "\nKSPBICG method was detected so the method could not "
                        "continue to enlarge the Krylov space.");
            PetscPrintf(PETSC_COMM_WORLD,
                        "\nTry to run again with another solver.\n");
        }
        else if (reason == KSP_DIVERGED_NONSYMMETRIC)
        {
            PetscPrintf(PETSC_COMM_WORLD,
                        "\nMatrix or preconditioner is unsymmetric but KSP "
                        "requires symmetric.\n");
        }
        else
        {
            PetscPrintf(PETSC_COMM_WORLD,
                        "\nDivergence detected, use command option "
                        "-ksp_monitor or -log_summary to check the details.\n");
        }
    }

#ifdef TEST_MEM_PETSC
    PetscMemoryGetCurrentUsage(&mem2);
    PetscPrintf(
        PETSC_COMM_WORLD,
        "###Memory usage by solver. Before: %f After: %f Increase: %d\n", mem1,
        mem2, (int)(mem2 - mem1));
#endif

    _elapsed_ctime += wtimer.elapsed();

    return converged;
}
コード例 #18
0
PetscErrorCode TSSetUp_Sundials(TS ts)
{
  TS_Sundials    *cvode = (TS_Sundials*)ts->data;
  PetscErrorCode ierr;
  PetscInt       glosize,locsize,i,flag;
  PetscScalar    *y_data,*parray;
  void           *mem;
  PC             pc;
  PCType         pctype;
  PetscBool      pcnone;

  PetscFunctionBegin;
  /* get the vector size */
  ierr = VecGetSize(ts->vec_sol,&glosize);CHKERRQ(ierr);
  ierr = VecGetLocalSize(ts->vec_sol,&locsize);CHKERRQ(ierr);

  /* allocate the memory for N_Vec y */
  cvode->y = N_VNew_Parallel(cvode->comm_sundials,locsize,glosize);
  if (!cvode->y) SETERRQ(PETSC_COMM_SELF,1,"cvode->y is not allocated");

  /* initialize N_Vec y: copy ts->vec_sol to cvode->y */
  ierr   = VecGetArray(ts->vec_sol,&parray);CHKERRQ(ierr);
  y_data = (PetscScalar*) N_VGetArrayPointer(cvode->y);
  for (i = 0; i < locsize; i++) y_data[i] = parray[i];
  ierr = VecRestoreArray(ts->vec_sol,NULL);CHKERRQ(ierr);

  ierr = VecDuplicate(ts->vec_sol,&cvode->update);CHKERRQ(ierr);
  ierr = VecDuplicate(ts->vec_sol,&cvode->ydot);CHKERRQ(ierr);
  ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->update);CHKERRQ(ierr);
  ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->ydot);CHKERRQ(ierr);

  /*
    Create work vectors for the TSPSolve_Sundials() routine. Note these are
    allocated with zero space arrays because the actual array space is provided
    by Sundials and set using VecPlaceArray().
  */
  ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)ts),1,locsize,PETSC_DECIDE,0,&cvode->w1);CHKERRQ(ierr);
  ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)ts),1,locsize,PETSC_DECIDE,0,&cvode->w2);CHKERRQ(ierr);
  ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->w1);CHKERRQ(ierr);
  ierr = PetscLogObjectParent((PetscObject)ts,(PetscObject)cvode->w2);CHKERRQ(ierr);

  /* Call CVodeCreate to create the solver memory and the use of a Newton iteration */
  mem = CVodeCreate(cvode->cvode_type, CV_NEWTON);
  if (!mem) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_MEM,"CVodeCreate() fails");
  cvode->mem = mem;

  /* Set the pointer to user-defined data */
  flag = CVodeSetUserData(mem, ts);
  if (flag) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVodeSetUserData() fails");

  /* Sundials may choose to use a smaller initial step, but will never use a larger step. */
  flag = CVodeSetInitStep(mem,(realtype)ts->time_step);
  if (flag) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetInitStep() failed");
  if (cvode->mindt > 0) {
    flag = CVodeSetMinStep(mem,(realtype)cvode->mindt);
    if (flag) {
      if (flag == CV_MEM_NULL) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMinStep() failed, cvode_mem pointer is NULL");
      else if (flag == CV_ILL_INPUT) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMinStep() failed, hmin is nonpositive or it exceeds the maximum allowable step size");
      else SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMinStep() failed");
    }
  }
  if (cvode->maxdt > 0) {
    flag = CVodeSetMaxStep(mem,(realtype)cvode->maxdt);
    if (flag) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_LIB,"CVodeSetMaxStep() failed");
  }

  /* Call CVodeInit to initialize the integrator memory and specify the
   * user's right hand side function in u'=f(t,u), the inital time T0, and
   * the initial dependent variable vector cvode->y */
  flag = CVodeInit(mem,TSFunction_Sundials,ts->ptime,cvode->y);
  if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVodeInit() fails, flag %d",flag);

  /* specifies scalar relative and absolute tolerances */
  flag = CVodeSStolerances(mem,cvode->reltol,cvode->abstol);
  if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVodeSStolerances() fails, flag %d",flag);

  /* Specify max num of steps to be taken by cvode in its attempt to reach the next output time */
  flag = CVodeSetMaxNumSteps(mem,ts->max_steps);

  /* call CVSpgmr to use GMRES as the linear solver.        */
  /* setup the ode integrator with the given preconditioner */
  ierr = TSSundialsGetPC(ts,&pc);CHKERRQ(ierr);
  ierr = PCGetType(pc,&pctype);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)pc,PCNONE,&pcnone);CHKERRQ(ierr);
  if (pcnone) {
    flag = CVSpgmr(mem,PREC_NONE,0);
    if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpgmr() fails, flag %d",flag);
  } else {
    flag = CVSpgmr(mem,PREC_LEFT,cvode->maxl);
    if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpgmr() fails, flag %d",flag);

    /* Set preconditioner and solve routines Precond and PSolve,
     and the pointer to the user-defined block data */
    flag = CVSpilsSetPreconditioner(mem,TSPrecond_Sundials,TSPSolve_Sundials);
    if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpilsSetPreconditioner() fails, flag %d", flag);
  }

  flag = CVSpilsSetGSType(mem, MODIFIED_GS);
  if (flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CVSpgmrSetGSType() fails, flag %d",flag);
  PetscFunctionReturn(0);
}
コード例 #19
0
    void TestBasicFunctionality() throw (Exception)
    {
        /*
         * We need to make sure here that the matrix is loaded with the appropriate parallel layout. Petsc's
         * default puts 1331 rows in each processor. This wouldn't be possible in a real bidomain simulation
         * because implies that equations V_665 an Phi_e_665 are solved in different processors.
         */
        unsigned num_nodes = 1331;
        DistributedVectorFactory factory(num_nodes);
        Vec parallel_layout = factory.CreateVec(2);

        Mat system_matrix;
        PetscTools::ReadPetscObject(system_matrix, "linalg/test/data/matrices/cube_6000elems_half_activated.mat", parallel_layout);

        PetscTools::Destroy(parallel_layout);

        // Set rhs = A * [1 0 1 0 ... 1 0]'
        Vec one_zeros = factory.CreateVec(2);
        Vec rhs = factory.CreateVec(2);

        for (unsigned node_index=0; node_index<2*num_nodes; node_index+=2)
        {
            PetscVecTools::SetElement(one_zeros, node_index, 1.0);
            PetscVecTools::SetElement(one_zeros, node_index+1, 0.0);
        }
        PetscVecTools::Finalise(one_zeros);

        MatMult(system_matrix, one_zeros, rhs);
        PetscTools::Destroy(one_zeros);

        LinearSystem ls = LinearSystem(rhs, system_matrix);

        ls.SetAbsoluteTolerance(1e-9);
        ls.SetKspType("cg");
        ls.SetPcType("none");

        ls.AssembleFinalLinearSystem();

        Vec solution = ls.Solve();

        DistributedVector distributed_solution = factory.CreateDistributedVector(solution);
        DistributedVector::Stripe vm(distributed_solution, 0);
        DistributedVector::Stripe phi_e(distributed_solution, 1);

        for (DistributedVector::Iterator index = distributed_solution.Begin();
             index!= distributed_solution.End();
             ++index)
        {
            /*
             * Although we're trying to enforce the solution to be [1 0 ... 1 0], the system is singular and
             * therefore it has infinite solutions. I've (migb) found that the use of different preconditioners
             * lead to different solutions ([0.8 -0.2 ... 0.8 -0.2], [0.5 -0.5 ... 0.5 -0.5], ...)
             *
             * If we were using PETSc null space, it would find the solution that satisfies x'*v=0,
             * being v the null space of the system (v=[1 1 ... 1])
             */
            TS_ASSERT_DELTA(vm[index] - phi_e[index], 1.0, 1e-6);
        }

        // Coverage (setting PC type after first solve)
        ls.SetPcType("blockdiagonal");

        PetscTools::Destroy(system_matrix);
        PetscTools::Destroy(rhs);
        PetscTools::Destroy(solution);

#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR <= 3) //PETSc 3.0 to PETSc 3.3
        //The PETSc developers changed this one, but later changed it back again!
        const PCType pc;
#else
        PCType pc;
#endif
        PC prec;
        KSPGetPC(ls.mKspSolver, &prec);
        PCGetType(prec, &pc);
        // Although we call it "blockdiagonal", PETSc considers this PC a generic SHELL preconditioner
        TS_ASSERT( strcmp(pc,"shell")==0 );

    }